IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v98y2014icp48-58.html
   My bibliography  Save this article

Markovian approximation to the finite loci coalescent with recombination along multiple sequences

Author

Listed:
  • Hobolth, Asger
  • Jensen, Jens Ledet

Abstract

The coalescent with recombination process has initially been formulated backwards in time, but simulation algorithms and inference procedures often apply along sequences. Therefore it is of major interest to approximate the coalescent with recombination process by a Markov chain along sequences. We consider the finite loci case and two or more sequences. We formulate a natural Markovian approximation for the tree building process along the sequences, and derive simple and analytically tractable formulae for the distribution of the tree at the next locus conditioned on the tree at the present locus. We compare our Markov approximation to other sequential Markov chains and discuss various applications.

Suggested Citation

  • Hobolth, Asger & Jensen, Jens Ledet, 2014. "Markovian approximation to the finite loci coalescent with recombination along multiple sequences," Theoretical Population Biology, Elsevier, vol. 98(C), pages 48-58.
    • Handle: RePEc:eee:thpobi:v:98:y:2014:i:c:p:48-58
    DOI: 10.1016/j.tpb.2014.01.002
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580914000033
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2014.01.002?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Thomas Mailund & Julien Y Dutheil & Asger Hobolth & Gerton Lunter & Mikkel H Schierup, 2011. "Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model," PLOS Genetics, Public Library of Science, vol. 7(3), pages 1-15, March.
    2. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Miroshnikov, Alexey & Steinrücken, Matthias, 2017. "Computing the joint distribution of the total tree length across loci in populations with variable size," Theoretical Population Biology, Elsevier, vol. 118(C), pages 1-19.
    2. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    3. Deng, Yun & Song, Yun S. & Nielsen, Rasmus, 2021. "The distribution of waiting distances in ancestral recombination graphs," Theoretical Population Biology, Elsevier, vol. 141(C), pages 34-43.
    4. Hobolth, Asger & Siri-Jégousse, Arno & Bladt, Mogens, 2019. "Phase-type distributions in population genetics," Theoretical Population Biology, Elsevier, vol. 127(C), pages 16-32.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
    2. Kevin J Liu & Jingxuan Dai & Kathy Truong & Ying Song & Michael H Kohn & Luay Nakhleh, 2014. "An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-13, June.
    3. Gideon S Bradburd & Peter L Ralph & Graham M Coop, 2016. "A Spatial Framework for Understanding Population Structure and Admixture," PLOS Genetics, Public Library of Science, vol. 12(1), pages 1-38, January.
    4. Juraj Bergman & Rasmus Ø. Pedersen & Erick J. Lundgren & Rhys T. Lemoine & Sophie Monsarrat & Elena A. Pearce & Mikkel H. Schierup & Jens-Christian Svenning, 2023. "Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Per Unneberg & Mårten Larsson & Anna Olsson & Ola Wallerman & Anna Petri & Ignas Bunikis & Olga Vinnere Pettersson & Chiara Papetti & Astthor Gislason & Henrik Glenner & Joan E. Cartes & Leocadio Blan, 2024. "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins," Nature Communications, Nature, vol. 15(1), pages 1-29, December.
    6. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    7. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Barton, N.H. & Etheridge, A.M. & Kelleher, J. & Véber, A., 2013. "Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks," Theoretical Population Biology, Elsevier, vol. 87(C), pages 105-119.
    9. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    10. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
    11. Jörn Bethune & April Kleppe & Søren Besenbacher, 2022. "A method to build extended sequence context models of point mutations and indels," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    12. Wilton, Peter R. & Baduel, Pierre & Landon, Matthieu M. & Wakeley, John, 2017. "Population structure and coalescence in pedigrees: Comparisons to the structured coalescent and a framework for inference," Theoretical Population Biology, Elsevier, vol. 115(C), pages 1-12.
    13. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    14. Kerdoncuff, Elise & Lambert, Amaury & Achaz, Guillaume, 2020. "Testing for population decline using maximal linkage disequilibrium blocks," Theoretical Population Biology, Elsevier, vol. 134(C), pages 171-181.
    15. Youjie Zhao & Chengyong Su & Bo He & Ruie Nie & Yunliang Wang & Junye Ma & Jingyu Song & Qun Yang & Jiasheng Hao, 2023. "Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    16. Xiaodong Liu & Long Lin & Mikkel-Holger S. Sinding & Laura D. Bertola & Kristian Hanghøj & Liam Quinn & Genís Garcia-Erill & Malthe Sebro Rasmussen & Mikkel Schubert & Patrícia Pečnerová & Renzo F. Ba, 2024. "Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    17. He Yu & Alexandra Jamieson & Ardern Hulme-Beaman & Chris J. Conroy & Becky Knight & Camilla Speller & Hiba Al-Jarah & Heidi Eager & Alexandra Trinks & Gamini Adikari & Henriette Baron & Beate Böhlendo, 2022. "Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    18. Kumagai, Seiji & Uyenoyama, Marcy K., 2015. "Genealogical histories in structured populations," Theoretical Population Biology, Elsevier, vol. 102(C), pages 3-15.
    19. Aoki, Kenichi & Wakano, Joe Yuichiro, 2022. "Hominin forager technology, food sharing, and diet breadth," Theoretical Population Biology, Elsevier, vol. 144(C), pages 37-48.
    20. Yuan Yin & Huizhong Fan & Botong Zhou & Yibo Hu & Guangyi Fan & Jinhuan Wang & Fan Zhou & Wenhui Nie & Chenzhou Zhang & Lin Liu & Zhenyu Zhong & Wenbo Zhu & Guichun Liu & Zeshan Lin & Chang Liu & Jion, 2021. "Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer," Nature Communications, Nature, vol. 12(1), pages 1-15, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:thpobi:v:98:y:2014:i:c:p:48-58. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.